I have no issues with with stroking the 2.8L to 2.9L. I just really want to avoid the harmonics issue at all cost, but would like to get as much power out if an N/A motor as possible. I will be doing extensive head work.

I think +1 mm on the intake valves and +2 mm on the exhaust valves. Port and polish the exhaust side for Euro M50B32 headers and polish the intake side and add the M54B30 Intake Manifold to complete the flow.

I also am going to convert to Solid Lifters and run a hotter set of cams that match the flow of the head. Probably looking at a custom set of cams.

I'm going to invite Adam (PEI330ci) into this thread...

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I think you've got a lot of enthusiasm....but have been mislead.

Stick with the 2.8L crank if you want to avoid serious harmonics...and I would not use an overheated block/head for any performance rebuild. Once you roast them, they are dead in my book.

I've done a lot of work on M54 heads, and I'll tell you that there are things you don't want to do like opening up the exhaust port too much. You won't match an S50 euro header without tunneling into the water jacket, but you'll get close. My advice is let the head porter decide how big to go...but be prepared to send him 2 cylinder heads to get it right. (Been there, done that)

Valve sizes: 1mm on the intake is fine, the exhaust I would leave OEM @ 30.5mm. I was told not to increase the exhaust valve size by a cylinder head guru, but I decided I "needed" to for my own reasons. The result: 31.5mm exhaust valves flow less than 30.5mm valves by a marginal amount.

I have no idea what your budget is...but I'll tell you that you are looking at close to $10k for the cylinder head work and valvetrain you have listed above. Solid lifters and custom cams adds about $6k to an already big price tag.